AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG025656

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG025656 MtrunA17_Chr5g0404131 90.377 239 12 5 1 232 71 305 3.75e-148 415
MsaG025656 MtrunA17_Chr8g0373231 55.556 243 82 8 1 232 1 228 3.27e-59 186
MsaG025656 MtrunA17_Chr1g0151461 38.889 90 52 2 89 177 155 242 2.45e-14 70.9
MsaG025656 MtrunA17_Chr7g0271861 56.250 48 19 1 119 166 18 63 2.75e-13 64.7
MsaG025656 MtrunA17_Chr2g0326771 40.000 60 36 0 96 155 189 248 8.24e-13 66.6
MsaG025656 MtrunA17_Chr4g0068031 67.568 37 12 0 123 159 30 66 1.06e-12 63.5
MsaG025656 MtrunA17_Chr4g0071301 69.048 42 12 1 111 152 181 221 1.40e-12 65.9
MsaG025656 MtrunA17_Chr4g0028961 32.143 84 52 1 72 155 186 264 1.08e-11 63.2
MsaG025656 MtrunA17_Chr1g0213161 62.857 35 13 0 121 155 150 184 1.84e-11 62.0
MsaG025656 MtrunA17_Chr5g0404981 38.571 70 41 1 88 155 263 332 5.76e-11 61.6
MsaG025656 MtrunA17_Chr1g0199671 62.162 37 14 0 119 155 238 274 6.40e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG025656 AT3G50870.1 41.281 281 104 10 5 232 9 281 1.66e-48 161
MsaG025656 AT4G36620.1 43.891 221 83 10 27 232 3 197 7.21e-39 134
MsaG025656 AT2G18380.1 41.304 230 93 8 19 230 2 207 1.69e-36 128
MsaG025656 AT5G56860.1 49.462 93 33 3 64 156 185 263 5.78e-17 79.3
MsaG025656 AT5G49300.1 53.731 67 27 2 98 162 11 75 4.49e-15 70.1
MsaG025656 AT4G26150.1 63.830 47 16 1 107 153 184 229 1.16e-13 69.7
MsaG025656 AT1G08010.2 45.070 71 33 2 105 170 203 272 1.38e-12 66.2
MsaG025656 AT1G08010.1 45.070 71 33 2 105 170 203 272 1.38e-12 66.2
MsaG025656 AT1G08010.3 45.070 71 33 2 105 170 203 272 1.38e-12 66.2
MsaG025656 AT3G54810.1 37.234 94 54 1 106 194 212 305 4.33e-12 65.1
MsaG025656 AT3G54810.2 37.234 94 54 1 106 194 212 305 4.33e-12 65.1
MsaG025656 AT5G26930.1 67.568 37 12 0 123 159 26 62 4.39e-12 61.6
MsaG025656 AT3G06740.1 71.429 35 10 0 125 159 43 77 7.18e-12 61.6
MsaG025656 AT3G20750.1 70.588 34 10 0 127 160 163 196 1.66e-11 62.0
MsaG025656 AT2G45050.1 36.585 82 45 2 74 155 137 211 7.10e-11 60.8
MsaG025656 AT4G34680.1 50.980 51 23 1 107 155 162 212 8.06e-11 60.8
MsaG025656 AT4G34680.2 50.980 51 23 1 107 155 162 212 8.06e-11 60.8

Find 48 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCAATCATGATTCTGAAAA+TGG 0.202815 5:+11071346 MsaT025656.1:CDS
GGAGTGAAACAATAGGTTTC+AGG 0.229794 5:-11070717 None:intergenic
GTTGGAGTTGTTGTTATTAT+TGG 0.243633 5:-11070931 None:intergenic
GAAGAAGAAGATGAAGAATT+AGG 0.286532 5:-11070738 None:intergenic
ATGGCATTCCATTTCTCTCT+TGG 0.336081 5:+11071365 MsaT025656.1:CDS
GAGAGAAACACTGCATCTTC+TGG 0.356763 5:-11071288 None:intergenic
AACGCCATCTATCGGCATAA+TGG 0.385803 5:+11071204 MsaT025656.1:CDS
CGGAACTCGTTAGTCATTGC+TGG 0.406108 5:-11071310 None:intergenic
TGTTCATGTGGTATGTTTCA+TGG 0.414708 5:+11070648 MsaT025656.1:CDS
CCACCTCCACACCGCTTTGG+AGG 0.424846 5:+11070994 MsaT025656.1:CDS
TAGGTTTCAGGTTCATCATA+AGG 0.424993 5:-11070705 None:intergenic
ATGCCGATAGATGGCGTTGC+CGG 0.430815 5:-11071199 None:intergenic
TAGAGTCTCCAAGAGAGAAA+TGG 0.442835 5:-11071373 None:intergenic
AGAATTAGGAGTGAAACAAT+AGG 0.458450 5:-11070724 None:intergenic
AGAAGAGCAACTGCTGCAGC+CGG 0.462808 5:+11071172 MsaT025656.1:CDS
ACACCACCTCCACACCGCTT+TGG 0.463073 5:+11070991 MsaT025656.1:CDS
GATTCCATTATGCCGATAGA+TGG 0.464364 5:-11071208 None:intergenic
CCTCCAAAGCGGTGTGGAGG+TGG 0.470303 5:-11070994 None:intergenic
TGAGTACTGTTGTACTGTTT+AGG 0.483115 5:-11070879 None:intergenic
CACTGCATCTTCTGGTTCTG+TGG 0.485352 5:-11071280 None:intergenic
AGCAAGAAGAGAATCATTGT+TGG 0.486549 5:-11070949 None:intergenic
GATTGGTTTCATCAATGAAA+CGG 0.487226 5:-11071330 None:intergenic
AACTGCTGCAGCCGGCACAC+CGG 0.491074 5:+11071180 MsaT025656.1:CDS
AGATGGCGTTGCCGGTGTGC+CGG 0.497703 5:-11071191 None:intergenic
ATCTCAAGGGCAACACGTGA+TGG 0.509206 5:+11070620 MsaT025656.1:CDS
TCCACACCGCTTTGGAGGAA+CGG 0.515774 5:+11070999 MsaT025656.1:CDS
GTTGATTGTACTCTTTCACT+TGG 0.527724 5:+11070762 MsaT025656.1:CDS
ATGATGCATCGTTCATCTCA+AGG 0.533388 5:+11070606 MsaT025656.1:CDS
CAGAACGACGTTCATGATGT+CGG 0.540322 5:-11070827 None:intergenic
ACACCGGCAACGCCATCTAT+CGG 0.547655 5:+11071196 MsaT025656.1:CDS
TCTCAAGGGCAACACGTGAT+GGG 0.577571 5:+11070621 MsaT025656.1:CDS
CAGTCACTATGCAATGCATG+TGG 0.582954 5:+11071127 MsaT025656.1:intron
ACCACCATCACAACAACTCA+TGG 0.584082 5:+11071248 MsaT025656.1:CDS
CAGTACTCAGTCTCAAACAA+AGG 0.584934 5:+11070893 MsaT025656.1:CDS
ATGAGTTGTTGTGATGGTGG+TGG 0.588375 5:-11071246 None:intergenic
TGATGCATCGTTCATCTCAA+GGG 0.590177 5:+11070607 MsaT025656.1:CDS
GTTCCTCCAAAGCGGTGTGG+AGG 0.595180 5:-11070997 None:intergenic
TCTTCAGTGAATCGAGTGGA+TGG 0.606627 5:-11070789 None:intergenic
GAACGGTCCACGAGGCCCAA+AGG 0.609147 5:+11071016 MsaT025656.1:CDS
ACCGTTCCTCCAAAGCGGTG+TGG 0.617219 5:-11071000 None:intergenic
TTCATCTTCAGTGAATCGAG+TGG 0.625964 5:-11070793 None:intergenic
ATGTGGGATCAGATTCAAGA+AGG 0.634149 5:+11071144 MsaT025656.1:CDS
ACCATGAGTTGTTGTGATGG+TGG 0.656581 5:-11071249 None:intergenic
AGTCACTATGCAATGCATGT+GGG 0.668102 5:+11071128 MsaT025656.1:intron
CGTACCATGAGTTGTTGTGA+TGG 0.677789 5:-11071252 None:intergenic
CGTGGACCGTTCCTCCAAAG+CGG 0.688334 5:-11071005 None:intergenic
CTTTGGAGGAACGGTCCACG+AGG 0.702547 5:+11071008 MsaT025656.1:CDS
GTGATGGGACACTGTTCATG+TGG 0.723745 5:+11070636 MsaT025656.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr5 gene 11070606 11071396 11070606 ID=MsaG025656
Chr5 mRNA 11070606 11071396 11070606 ID=MsaT025656.1;Parent=MsaG025656
Chr5 exon 11070606 11071037 11070606 ID=MsaT025656.1.exon1;Parent=MsaT025656.1
Chr5 CDS 11070606 11071037 11070606 ID=cds.MsaT025656.1;Parent=MsaT025656.1
Chr5 exon 11071130 11071396 11071130 ID=MsaT025656.1.exon2;Parent=MsaT025656.1
Chr5 CDS 11071130 11071396 11071130 ID=cds.MsaT025656.1;Parent=MsaT025656.1
Gene Sequence

>MsaT025656.1

ATGATGCATCGTTCATCTCAAGGGCAACACGTGATGGGACACTGTTCATGTGGTATGTTTCATGGACAAAACAACTCATTCTCAATGTTATTCTCTACACCTTATGATGAACCTGAAACCTATTGTTTCACTCCTAATTCTTCATCTTCTTCTTCTGTTGATTGTACTCTTTCACTTGGAACACCATCCACTCGATTCACTGAAGATGAAGAGAAAAGAAGCCGACATCATGAACGTCGTTCTGTCAAAAATTTCTGTTGGGATTTGCTAACACCTAAACAGTACAACAGTACTCAGTCTCAAACAAAGGCAACACGTGCAAATACCAATAATAACAACAACTCCAACAATGATTCTCTTCTTGCTCGTAGATGTGCAAACTGTGACACCACCTCCACACCGCTTTGGAGGAACGGTCCACGAGGCCCAAAGTCACTATGCAATGCATGTGGGATCAGATTCAAGAAGGAAGAGAGAAGAGCAACTGCTGCAGCCGGCACACCGGCAACGCCATCTATCGGCATAATGGAATCAGCTTCGATGTATAACCACCACCATCACAACAACTCATGGTACGTACAACCACAGAACCAGAAGATGCAGTGTTTCTCTCCAGCAATGACTAACGAGTTCCGTTTCATTGATGAAACCAATCATGATTCTGAAAATGGCATTCCATTTCTCTCTTGGAGACTCTAA
Protein sequence

>MsaT025656.1

MMHRSSQGQHVMGHCSCGMFHGQNNSFSMLFSTPYDEPETYCFTPNSSSSSSVDCTLSLGTPSTRFTEDEEKRSRHHERRSVKNFCWDLLTPKQYNSTQSQTKATRANTNNNNNSNNDSLLARRCANCDTTSTPLWRNGPRGPKSLCNACGIRFKKEERRATAAAGTPATPSIGIMESASMYNHHHHNNSWYVQPQNQKMQCFSPAMTNEFRFIDETNHDSENGIPFLSWRL*